The Department of Agriculture has denied covering up the circumstances surrounding the mass death of more than 4000 sheep on a voyage to the Middle East.

Most of the sheep died on an afternoon of extreme heat 15 days after leaving Fremantle on board the Livestock Shipping Services Pty Ltd–operated Bader III.

Documents obtained under Freedom of Information show the exporter then took 13 days to officially notify the DoA that the mortality rate on the horror voyage exceeded reportable limits.

Australian laws governing the issuing of export licences, require exporters to notify authorities as soon as possible or within 12 hours.

Sheep being loaded onto the Bader III in Fremantle. Picture: File

Other documents show the on-board veterinarian employed by LSS did not provide daily reports to authorities as required under the laws.

The DoA, which made no adverse findings against LSS after investigating the incidents, rejected claims from Animals Australia that it covered up the reporting delay and the lack of daily updates.

The official DoA report did not mention either issue. It also failed to name the exporter or the Bader III, which is understood to have left Fremantle late yesterday with more livestock for the Middle East.

The DoA and LSS remained publicly silent on the death of 4179 of the 75,508 sheep on the vessel last year for more than four months, and only commented after the incident was revealed by The West Australian in January.

FOI documents from September 6 last year show the on-board veterinarian reported the sheep were “travelling well” but the Bader III had started “zigzagging” to improve ventilation.

Hours later thousands were dead and the ship had docked at Doha in Qatar.

The ship spent three days unloading livestock in Doha with dead sheep littering the decks. Australian authorities received no hint that anything was wrong.

The ship was back at sea on September 11 when it was noted in the daily report that “overall mortality may exceed two per cent”. This daily report and those for the days that followed were not received by the DoA until September 16.

After dumping the carcasses at sea and taking six days to cover the short distance between Doha and the United Arab Emirates, the Bader III docked and the remaining livestock was unloaded.

LSS notified DoA of high morality rate on September 19. On September 20, LSS received an email from a senior DoA official which spelt out the laws regarding export licences and asked a series of questions about the conduct of the voyage.

LSS said it complied fully and in good faith with the requirements of the DoA investigation.

“The investigation into the incident identified that an extreme weather event caused heat stress leading to the reportable mortality incident,” it said in a statement.

“LSS has adopted the recommendations and findings from the investigation in order to improve its heat-stress risk management.”

Animals Australia accused DoA of a chronic failure to properly regulate the live export industry."

Spokeswoman Lisa Chalk said heat stress was a shocking way for an animal to die and the sheep would have literally been “cooked alive”.

“The Australian Government was kept in the dark for nearly two weeks while the disaster was unfolding despite the exporter’s legal obligations to report the high number of deaths immediately,” she said.